A MOLECULAR MODELING STUDY OF GENERATION-DEPENDENT STABILITY OF DENDRITIC POLYSILANES

2008 ◽  
Vol 07 (05) ◽  
pp. 923-931 ◽  
Author(s):  
TING MU ◽  
DACHENG FENG ◽  
SHENGYU FENG
Keyword(s):  
Molecular Dynamics ◽  
Molecular Modeling ◽  
Molecular Dynamics Simulations ◽  
Silicon Atom ◽  
Minimum Energy ◽  
Core Structure ◽  
The Core ◽  
Molecular Modeling Study ◽  
Dynamics Simulations ◽  
Energy Configurations

This paper focuses on the maximum generation issue. Molecular dynamics simulations have been employed to search the minimum energy configurations of eight types of structurally related polysilane dendrimers of various generations. Calculations reveal that for the studied dendrimers, the innermost Si – Si bonds adjoining the silicon atom at the center of the core structure are extended for steric relief with the amount of extension increasing with the number of generations due to the rise of the spatial hindrance inside these molecules.

Structural stability of CmTin microclusters and nanoparticles: Molecular–dynamics simulations

2005 ◽  
Vol 1 (4) ◽  
pp. 204-209
Author(s):  
O.B. Malcıoğlu ◽  
Ş. Erkoç
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Binary Systems ◽  
Minimum Energy ◽  
Potential Energy Function ◽  
Md Simulations ◽  
Atomic Interactions ◽  
Dynamics Simulations ◽  
Three Body ◽  
Initial Geometry

The minimum energy structures of CmTin microclusters and nanoparticles have been investigated theoretically by performing molecular–dynamics (MD) simulations. Selected crystalline and completely random initial geometries are considered. The potential energy function (PEF) used in the calculations includes two– and three–body atomic interactions for C-Ti binary systems. Molecular–dynamics simulations have been performed at 1 K and 300 K. It has been found that initial geometry has a very strong influence on relaxed geometry

ON THE STRUCTURAL AND ENERGETIC FEATURES OF SMALL METAL CLUSTERS: Nin, Cun, Pdn, Ptn, AND Pbn; n=3–13

2004 ◽  
Vol 15 (06) ◽  
pp. 917-930 ◽  
Author(s):  
ZUHEIR EL-BAYYARI ◽  
HÜSEYIN OYMAK ◽  
HATICE KÖKTEN
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Molecular Dynamics Simulations ◽  
Energy Function ◽  
Metal Clusters ◽  
Minimum Energy ◽  
Potential Energy Function ◽  
Empirical Potential ◽  
Dynamics Simulations

Using an empirical potential energy function parametrized for each of the Ni , Cu , Pd , Pt , and Pb systems, minimum-energy structures of Ni n, Cu n, Pd n, Pt n, and Pb n (n=3–13) microclusters have been determined by performing molecular-dynamics simulations. The structural and energetic features of the obtained microclusters have been investigated.

Molecular Modeling Studies of Anti-Alzheimer Agents by QSAR, Molecular Docking and Molecular Dynamics Simulations Techniques

2020 ◽  
Vol 16 (7) ◽  
pp. 903-927 ◽  
Author(s):  
Rahman Abdizadeh ◽  
Farzin Hadizadeh ◽  
Tooba Abdizadeh
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Modeling ◽  
Molecular Dynamics Simulations ◽  
Data Set ◽  
Ache Inhibitors ◽  
Modeling Studies ◽  
Qsar Models ◽  
Molecular Modeling Studies ◽  
Dynamics Simulations

Background: Acetylcholinesterase (AChE), a serine hydrolase, is an important drug target in the treatment of Alzheimer's disease (AD). Thus, novel AChE inhibitors were designed and developed as potential drug candidates, for significant therapy of AD. Objective: In this work, molecular modeling studies, including CoMFA, CoMFA-RF, CoMSIA, HQSAR and molecular docking and molecular dynamics simulations were performed on a series of AChE inhibitors to get more potent anti-Alzheimer drugs. Methods: 2D/3D-QSAR models including CoMFA, CoMFA-RF, CoMSIA, and HQSAR methods were carried out on 40 pyrimidinylthiourea derivatives as data set by the Sybylx1.2 program. Molecular docking and molecular dynamics simulations were performed using the MOE software and the Sybyl program, respectively. Partial least squares (PLS) model as descriptors was used for QSAR model generation. Results: The CoMFA (q2, 0.629; r2ncv, 0.901; r2pred, 0.773), CoMFA-RF (q2, 0.775; r2ncv, 0.910; r2pred, 0.824), CoMSIA (q2, 0.754; r2ncv, 0.919; r2pred, 0.874) and HQSAR models (q2, 0.823; r2ncv, 0.976; r2pred, 0.854) for training and test set yielded significant statistical results. Conclusion: These QSAR models were excellent, robust and had good predictive capability. Contour maps obtained from the QSAR models were validated by molecular dynamics simulationassisted molecular docking study. The resulted QSAR models could be useful for the rational design of novel potent AChE inhibitors in Alzheimer's treatment.

Sign in / Sign up

Export Citation Format

Share Document